##compute the number of ADDITIONAL threads to be used (--cpu)
        addthreads=\${GALAXY_SLOTS:-1} && (( addthreads-- )) &&
    

#if $input_hmm_conditional.input_hmm_source == "history":
    #set $input_hmm_filename = "localref.hmm"
    ln -s '${input_hmm_conditional.hmmfile}' '${input_hmm_filename}' &&
    ## "Press" database
    hmmpress '${input_hmm_filename}' &&
#else:
    #set $input_hmm_filename = str($input_hmm_conditional.index.fields.db_path)
#end if
  
nhmmscan


#if $oformat:
    #for o in str($oformat).split(','):
        --$o '$getVar($o, 'MISSING_OUTPUT'+$o)'
    #end for
#end if
$acc $noali $notextw
  

#if $repopt.repopt_sel == "evalue"
  -E $repopt.E
  #if str($repopt.incE) != ""
    --incE $repopt.incE
  #end if
#elif $repopt.repopt_sel == "score"
  -T $repopt.T
  #if str($repopt.incT) != ""
    --incT $repopt.incT
  #end if
#else
  $repopt.repopt_sel
#end if
  

$max
--F1 $F1
--F2 $F2
--F3 $F3
$nobias
  
--B1 $B1
--B2 $B2
--B3 $B3


$nonull2

#if str($Z):
    -Z $Z
#end if

#if str($domZ):
    --domZ $domZ
#end if
  

#if str($w_beta):
    --w_beta $w_beta
#end if

#if str($w_length):
    --w_length $w_length
#end if
  

      --cpu \$addthreads
  

      --seed $seed
  

'$input_hmm_filename'
'$seqfile'
> '$output'